A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.Comment: 5 pages, 3 figures. Chan CX, Beiko RG and Ragan MA (2007). A two-phase approach for detecting recombination in nucleotide sequences. In Hazelhurst S and Ramsay M (Eds) Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January, Johannesburg, 9-1

On Bruen chains

It is known that a Bruen chain of the three-dimensional projective space $\mathrm{PG}(3,q)$ exists for every odd prime power $q$ at most $37$, except for $q=29$. It was shown by Cardinali et. al (2005) that Bruen chains do not exist for $41\le q\leq 49$. We develop a model, based on finite fields, which allows us to extend this result to $41\leqslant q \leqslant 97$, thereby adding more evidence to the conjecture that Bruen chains do not exist for $q>37$. Furthermore, we show that Bruen chains can be realised precisely as the $(q+1)/2$-cliques of a two related, yet distinct, undirected simple graphs

Some sporadic translation planes of order 11211^2

In \cite{PK}, the authors constructed a translation plane $\Pi$ of order $11^2$ arising from replacement of a sporadic chain $F'$ of reguli in a regular spread $F$ of $PG(3,11)$. They also showed that two more non isomorphic translation planes, called  $\Pi_1$ and $\Pi_{13}$, arise respectively by derivation and double derivation in $F\setminus F'$ which correspond to a further replacement of a regulus with its opposite regulus and a pair of reguli with their opposite reguli, respectively.  In \cite{AL}, the authors proved that the translation complement of $\Pi$ contains a subgroup isomorphic to \SL(2,5). Here, the full collineation group of each of the planes $\Pi$, $\Pi_1$ and $\Pi_{13}$ is determined

Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event

The True Meaning of Going Armed in the Statute of Northampton: A Response to Patrick J. Charles

In the debate over the meaning of the right to keep and bear arms guaranteed by the Second Amendment, some writers have argued that the prohibition in the 1328 English Statute of Northampton on going armed referred to carrying weapons, thus purportedly showing that regulation of carrying weapons was well known and established when the Second Amendment was adopted. For the first time, this Article reveals, through a thorough analysis of medieval royal proclamations and acts of parliament, well-regarded legal treatises, literature of the time, and English case law, that going armed did not refer to carrying weapons, but rather to wearing armor. Accordingly, the Statute of Northampton does not show that regulation of carrying weapons was established at the time of the adoption of the Second Amendment

Streets of Galway: the challenge of adapting for television Ken Bruen's Jack Taylor novels

[Abstract] Literature and identity are two ideas intrinsically linked. There is an indivisible relationship between both concepts and neither can advance without the other. Literary manifestations have been worked as a tool for the construction and expression of personal as well as collective identity. In the Irish case, the crime novel is a vital element to reflect Irish identity. This piece of research analyses and contrasts the crime novels The Guards and The Magdalen Martyrs written by Ken Bruen with its expansion into television Jack Taylor on Netflix. As such, the methodology used is firstly based on a socio-historical analysis as well as the study of the development of the Irish crime novel in recent years to, secondly, expose a comparison between written and audiovisual material. The main objective is to establish a framework to understand the differences and similarities about how Irish identity and the main character are relocated in front of the viewers. The idea of this literary analysis is to test whether cinematic art can show identity at the same level as literature.Traballo fin de grao (UDC.FIL). Inglés: estudios lingüísticos y literarios. Curso 2020/202